Not so fast, even the person who coined the term microbiome (Josh Lederberg) who originally seemed to use it to refer to all the genomes of the microbes also used the term ambiguously (e.g., in one paper he sad "the microbiome flora" meaning I guess the microbiota.

Is it plausible to speculate that this ecosystem is capable of modulating the behavior of the host to get more food (as in obesity where the microbiome is altered), or even affecting how we behave in other situations?

In a commentary published in August in the journal Nature, he asserted that antibiotics are permanently altering microbial flora of the human body, also known as the microbiome or microbiota, with serious health consequences.